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Gonzalez CG, Mills RH, Zhu Q, Sauceda C, Knight R, Dulai PS, Gonzalez DJ. Location-specific signatures of Crohn's disease at a multi-omics scale. Microbiome 2022; 10:133. [PMID: 35999575 PMCID: PMC9400277 DOI: 10.1186/s40168-022-01331-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/15/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Crohn's disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments. RESULTS Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin. CONCLUSIONS When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD's strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology. Video Abstract.
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Affiliation(s)
- Carlos G Gonzalez
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Consuelo Sauceda
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Parambir S Dulai
- Department of Medicine, Division of Gastroenterology and Hepatology, Feinberg School of Medicine Northwestern University, Chicago, IL, 60061, USA.
| | - David J Gonzalez
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA.
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA.
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA.
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